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Hello, I've tested this,it's ok on my environment. I don't know why the PCI device 0000:04:00.0 is being assigned to the second instance, it should be the PCI device 0000:04:00.1. I think you need to look at the pci_devices table of nova DB. After my test, it's as below on my environment:

mysql> select * from pci_devices; +---------------------+---------------------+------------+---------+----+-----------------+--------------+------------+-----------+----------+------------------+-----------------+-----------+------------+--------------------------------------+ | created_at | updated_at | deleted_at | deleted | id | compute_node_id | address | product_id | vendor_id | dev_type | dev_id | label | status | extra_info | instance_uuid | +---------------------+---------------------+------------+---------+----+-----------------+--------------+------------+-----------+----------+------------------+-----------------+-----------+------------+--------------------------------------+ | 2014-02-22 06:59:16 | 2014-02-24 09:47:58 | NULL | 0 | 1 | 1 | 0000:02:00.0 | 10c9 | 8086 | type-PCI | pci_0000_02_00_0 | label_8086_10c9 | allocated | {} | 23749835-30bd-43fc-9a37-e21609a30e70 | | 2014-02-22 06:59:16 | 2014-02-24 09:49:06 | NULL | 0 | 2 | 1 | 0000:02:00.1 | 10c9 | 8086 | type-PCI | pci_0000_02_00_1 | label_8086_10c9 | allocated | {} | 5864a793-e96e-4ffd-bd84-9a3ada2ef9b4 | | 2014-02-22 06:59:16 | NULL | NULL | 0 | 3 | 1 | 0000:03:00.0 | 10c9 | 8086 | type-PCI | pci_0000_03_00_0 | label_8086_10c9 | available | {} | NULL | | 2014-02-22 06:59:16 | NULL | NULL | 0 | 4 | 1 | 0000:03:00.1 | 10c9 | 8086 | type-PCI | pci_0000_03_00_1 | label_8086_10c9 | available | {} | NULL | +---------------------+---------------------+------------+---------+----+-----------------+--------------+------------+-----------+----------+------------------+-----------------+-----------+------------+--------------------------------------+